Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nkx2-1

Cell type

Cell type Class
Lung
Cell type
Lung
MeSH Description
Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.

Attributes by original data submitter

Sample

source_name
Lung tissue
chip antibody
NKX2-1 (ab133737, Abcam)
age
10 wk
cell type
AT1
replicate
1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole lung ChIP-seq were performed as described in the associated paper and cell type specific ChIp-seqs were performed on chromatin from sorted nulcei based on a SunGFP reporter induced by recombination undercontrol of cell type specific Cre or CreERs. ChIP DNA quantity was measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851). 2-5ng of sample DNA was used to generate sequencing libraries using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Step 3.1 in the NEB protocol was skipped to improve sample retention per manufacturer's recommendation. Samples were PCR amplified for 12 cycles and barcoded using indexing primers (New England BioLabs, E7335s or E7500S) followed by a final (.65 x -1 x bead volume) size selection and purification step using a SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size by gel electrophoresis and concentration measured using the Qubit HS dsDNA assay. Samples were then sequenced on the Illumina NextSeq500.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
26437418
Reads aligned (%)
92.9
Duplicates removed (%)
27.3
Number of peaks
44205 (qval < 1E-05)

mm9

Number of total reads
26437418
Reads aligned (%)
92.5
Duplicates removed (%)
27.3
Number of peaks
44167 (qval < 1E-05)

Base call quality data from DBCLS SRA